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United States Department of Agriculture

Agricultural Research Service

Research Project: Utilization of Genomics for Improving Production Traits in Cool and Cold Water Aquaculture

Location: Cool and Cold Water Aquaculture Research

2013 Annual Report


1a.Objectives (from AD-416):
1. Identify genes affecting variation in production traits in rainbow trout through QTL mapping and functional genomic (i.e. expression based) approaches. • 1.a. Detect and fine map quantitative trait loci for resistance to bacterial cold water disease in rainbow trout. • 1.b. Fine map quantitative trait loci affecting response to crowding stress. • 1.c. Identify genes affecting response to crowding stress through functional genomic approaches. • 1.d. Evaluate performance of fish differing in stress response phenotypes. • 1.e. Identify genes affecting carcass quality traits in rainbow trout. • 1.f. Identify and characterize key oocyte-expressed genes/microRNAs important for folliculogenesis and early development.

2: Develop genomic tools and resources to facilitate the use of state of the art approaches for genetic improvement of rainbow trout. • 2.a. Facilitate the identification of genes affecting production traits by producing a second generation bacterial artificial chromosome (BAC) map which is anchored to the genetic map. • 2.b. Develop single nucleotide polymorphic (SNP) markers to enhance fine mapping and enable genomic selection for rainbow trout. • 2.c. Identification of microRNAs that affect expression of genes controlling production traits in rainbow trout.

3: Develop database to store, and facilitate analysis of genotypic and phenotypic data.


1b.Approach (from AD-416):
The demand for seafood is increasing worldwide while captured fisheries harvest is limited and unsustainable. To meet increasing consumer demand, U.S. aquaculture producers have to achieve improved efficiencies and sustainable practices while maintaining and improving product quality. The application of genomic technologies towards the genetic improvement of aquaculture species is expected to facilitate selective breeding and provide basic information on the biochemical mechanisms controlling traits of interest. In collaboration with U.S. and international scientists, we have developed a suite of genome tools and reagents for rainbow trout to identify and characterize genes affecting aquaculture production traits. Projects concurrent with our previous 5-year project characterized the genetic variation of the National Center for Cool and Cold Water Aquaculture (NCCCWA) broodstock with respect to resistance to Bacterial Cold Water Disease (BCWD) and response to crowding stress. Specific crosses were identified to facilitate the identification of genes affecting these traits through genetic mapping and functional genomic approaches. The current project will improve and utilize genome mapping approaches to identify positional candidate genes affecting these traits. This genetic information will be used for improving our understanding of the genetics of disease resistance and production traits and could be transferred to the US industry through improved germplasm. In addition, possibilities for developing informative crosses and functional genomic approaches which target the identification of genes affecting carcass quality traits will be determined. We will also continue to identify and characterize genes in the oocyte (pre-mature egg) which impact embryonic development and egg quality traits important to breeders.


3.Progress Report:
Approximately 5,000 new genetic markers representing the entire rainbow trout genome were used to validate the presence of chromosome regions harboring genes with moderate to large effect on this trait. The same new genetic markers system was used to validate and identify new chromosome regions affecting stress response to handling and crowding in rainbow trout. Fish response to stress is an important factor in aquaculture production, having significant negative impacts on growth, feed efficiency, immune response, and reproductive characteristics.

Development of new robust genotyping platform for rainbow trout. A relative new technology termed “Restriction-site associated DNA” (RAD) was used to identify a set of 150,000 single nucleotide polymorphisms (SNPs), a type of genetic marker defined as single base pair differences in DNA sequences between individuals. A genotyping assay tool termed “SNP Chip” was designed for rainbow trout. It is composed of 57,500 SNPs taken primarily from the RAD-SNPs dataset we generate, but also by using datasets generated by US and international collaborators. We are currently validating the utility and efficacy of this tool for genetic analyses in rainbow trout.

The National Center for Cool and Cold Water Aquaculture's database was modified to analyze high volumes of DNA and/or RNA sequence data associated with state of the art gene expression and mapping technologies. Also, the database was updated with fish pedigree and performance information associated with stress response and disease resistance.


Review Publications
Shirak, A., Palti, Y., Bern, O., Kocher, T.D., Hulata, G., Ron, M., Avtalion, R. 2013. A deleterious effect associated with UNH159 is attenuated in twin embryos of an inbred line of tilapia (Oreochromis aureus). Journal of Fish Biology. 82:42-53.

Rexroad III, C.E., Vallejo, R.L., Liu, S., Palti, Y., Weber, G.M. 2012. QTL affecting stress response to crowding in a rainbow trout broodstock population . BioMed Central (BMC) Genetics. 13:97. DOI:10.1186/1471-2156-13-97

Wolters, W.R., Burr, G.S., Palti, Y., Vallejo, R.L. 2013. Phenotypic and genetic variation in two North American arctic charr (Salvelinus alpinus) stocks cultured in recirculating aquaculture systems. Journal of the World Aquaculture Society. 44:476:485.

Rexroad III, C.E., Vallejo, R.L., Liu, S., Palti, Y., Weber, G.M. 2013. Quantitative trait loci affecting response to crowding stress in an F2 generation of rainbow trout produced through phenotypic selection. Marine Biotechnology. 15(5): 613-627: DOI 10.1007/s10126-013-9512-5.

Wang, L., Tripurani, S.K., Wanna, W., Rexroad III, C.E., Yao, J. 2013. Cloning and characterization of a novel oocyte-specific gene encoding an F-Box protein in rainbow trout (Oncorhynchus mykiss). Reproductive Biology and Endocrinology. 11:86.DOI: 10.1186/1477-7827-11-86.

Last Modified: 11/24/2014
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